1. CHAPTER 20 DNA TECHNOLOGY AND GENOMICS Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Section C: Practical Applications of DNA Technology 1.DNA technology is reshaping medicine and the pharmaceutical industry 2. DNA technology offers forensic, environmental, and agricultural applications 3. DNA technology raises important safety and ethical questions

2. Modern biotechnology is making enormous contributions to both the diagnosis of diseases and in the development of pharmaceutical products. The identification of genes whose mutations are responsible for genetic diseases could lead to ways to diagnose, treat, or even prevent these conditions. Susceptibility to many “nongenetic” diseases, from arthritis to AIDS, is influenced by a person’s genes. Diseases of all sorts involve changes in gene expression. DNA technology can identify these changes and lead to the development of targets for prevention or therapy. 1. DNA technology is reshaping medicine and the pharmaceutical industry Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

3. PCR and labeled probes can track down the pathogens responsible for infectious diseases. For example, PCR can amplify and thus detect HIV DNA in blood and tissue samples, detecting an otherwise elusive infection. Medical scientists can use DNA technology to identify individuals with genetic diseases before the onset of symptoms, even before birth. It is also possible to identify symptomless carriers. Genes have been cloned for many human diseases, including hemophilia, cystic fibrosis, and Duchenne muscular dystrophy. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

4. Hybridization analysis makes it possible to detect abnormal allelic forms of genes, even in cases in which the gene has not yet been cloned. The presence of an abnormal allele can be diagnosed with reasonable accuracy if a closely linked RFLP marker has been found. The closeness of the marker to the gene makes crossing over between them unlikely and the marker and gene will almost always stay together in inheritance. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.15

5. Techniques for gene manipulation hold great potential for treating disease by gene therapy. This alters an afflicted individual’s genes. A normal allele is inserted into somatic cells of a tissue affected by a genetic disorder. For gene therapy of somatic cells to be permanent, the cells that receive the normal allele must be ones that multiply throughout the patient’s life. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

6. Bone marrow cells, which include the stem cells that give rise to blood and immune system cells, are prime candidates for gene therapy. A normal allele could be inserted by a viral vector into some bone marrow cells removed from the patient. If the procedure succeeds, the returned modified cells will multiply throughout the patient’s life and express the normal gene, providing missing proteins. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.16

7. Despite “hype” in the news media over the past decade, there has been very little scientifically strong evidence of effective gene therapy. Even when genes are successfully and safely transferred and expressed in their new host, their activity typically diminishes after a short period. Most current gene therapy trials are directed not at correcting genetic defects, but to fight major killers such as heart disease and cancer. The most promising trials are those in which a limited activity period is not only sufficient but desirable. Some success has been reported in stimulated new heart blood vessels in pigs after gene therapy. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

8. Gene therapy poses many technical questions. These include regulation of the activity of the transferred gene to produce the appropriate amount of the gene product at the right time and place. In addition, the insertion of the therapeutic gene must not harm some other necessary cell function. Gene therapy raises some difficult ethical and social questions. Some critics suggest that tampering with human genes, even for those with life-threatening diseases, is wrong. They argue that this will lead to the practice of eugenics, a deliberate effort to control the genetic makeup of human populations. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

9. The most difficult ethical question is whether we should treat human germ-line cells to correct the defect in future generations. In laboratory mice, transferring foreign genes into egg cells is now a routine procedure. Once technical problems relating to similar genetic engineering in humans are solved, we will have to face the question of whether it is advisable, under any circumstances, to alter the genomes of human germ lines or embryos. Should we interfere with evolution in this way? Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

10. From a biological perspective, the elimination of unwanted alleles from the gene pool could backfire. Genetic variation is a necessary ingredient for the survival of a species as environmental conditions change with time. Genes that are damaging under some conditions could be advantageous under other conditions, for example the sickle-cell allele. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

11. DNA technology has been used to create many useful pharmaceuticals, mostly proteins. By transferring the gene for a protein into a host that is easily grown in culture, one can produce large quantities of normally rare proteins. By including highly active promotors (and other control elements) into vector DNA, the host cell can be induced to make large amounts of the product of a gene into the vector. In addition, host cells can be engineered to secrete a protein, simplifying the task of purification. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

12. One of the first practical applications of gene splicing was the production of mammalian hormones and other mammalian regulatory proteins in bacteria. These include human insulin and growth factor (HFG). Human insulin, produced by bacteria, is superior for the control of diabetes than the older treatment of pig or cattle insulin. Human growth hormone benefits children with hypopituitarism, a form of dwarfism. Tissue plasminogen activator (TPA) helps dissolve blood clots and reduce the risk of future heart attacks. However, like many such drugs, it is expensive. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

13. New pharmaceutical products are responsible for novel ways of fighting diseases that do not respond to traditional drug treatments. One approach is to use genetically engineered proteins that either block or mimic surface receptors on cell membranes. For example, one experimental drug mimics a receptor protein that HIV bonds to when entering white blood cells, but HIV binds to the drug instead and fails to enter the blood cells. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

14. Virtually the only way to fight viral diseases is by vaccination. A vaccine is a harmless variant or derivative of a pathogen that stimulates the immune system. Traditional vaccines are either particles of virulent viruses that have been inactivated by chemical or physical means or active virus particles of a nonpathogenic strain. Both are similar enough to the active pathogen to trigger an immune response. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

15. Recombinant DNA techniques can generate large amounts of a specific protein molecule normally found on the pathogen’s surface. If this protein triggers an immune response against the intact pathogen, then it can be used as a vaccine. Alternatively, genetic engineering can modify the genome of the pathogen to attenuate it. These attenuated microbes are often more effective than a protein vaccine because it usually triggers a greater response by the immune system. Pathogens attenuated by gene-splicing techniques may be safer than the natural mutants traditionally used. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

16. In violent crimes, blood, semen, or traces of other tissues may be left at the scene or on the clothes or other possessions of the victim or assailant. If enough tissue is available, forensic laboratories can determine blood type or tissue type by using antibodies for specific cell surface proteins. However, these tests require relatively large amounts of fresh tissue. Also, this approach can only exclude a suspect. 2. DNA technology offers forensic, environmental, and agricultural applications Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

17. DNA testing can identify the guilty individual with a much higher degree of certainty, because the DNA sequence of every person is unique (except for identical twins). RFPL analysis by Southern blotting can detect similarities and differences in DNA samples and requires only tiny amount of blood or other tissue. Radioactive probes mark electrophoresis bands that contain certain RFLP markers. Even as few as five markers from an individual can be used to create a DNA fingerprint. The probability that two people (that are not identical twins) have the same DNA fingerprint is very small. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

18. DNA fingerprints can be used forensically to presence evidence to juries in murder trials. This autoradiograph of RFLP bands of samples from a murder victim, the defendant, and the defendant’s clothes is consistent with the conclusion that the blood on the clothes is from the victim, not the defendant. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.17

19. The forensic use of DNA fingerprinting extends beyond violent crimes. For instance, DNA fingerprinting can be used to settle conclusively a question of paternity. These techniques can also be used to identify the remains of individuals killed in natural or man-made disasters. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

20. Variations in the lengths of satellite DNA are increasingly used as markers in DNA fingerprinting. The most useful satellites are microsatellites, which are roughly 10 to 100 base pairs long. They have repeating units of only a few base pairs and are highly variable from person to person. Individuals may vary in the numbers of repeats, simple tandem repeats (STRs), at a locus. Restriction fragments with STRs vary in size among individuals because of differences in STR lengths. PCR is often used to amplify selectively particular STRs or other markers before electrophoresis, especially if the DNA is poor or in minute quantities. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

21. The DNA fingerprint of an individual would be truly unique if it were feasible to perform restriction fragment analysis on the entire genome. In practice, forensic DNA tests focus on only about five tiny regions of the genome. The probability that two people will have identical DNA fingerprints in these highly variable regions is typically between one in 100,000 and one in a billion. The exact figure depends on the number of markers and the frequency of those markers in the population. Despite problems that might arise from insufficient statistical data, human error, or flawed evidence, DNA fingerprinting is now accepted as compelling evidence. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

22. Increasingly, genetic engineering is being applied to environmental work. Scientists are engineering the metabolism of microorganisms to help cope with some environmental problems. For example genetically engineered microbes that can extract heavy metals from their environments and incorporate the metals into recoverable compounds may become important both in mining materials and cleaning up highly toxic mining wastes. In addition to the normal microbes that participate in sewage treatment, new microbes that can degrade other harmful compounds are being engineered. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

23. For many years scientists have been using DNA technology to improve agricultural productivity. DNA technology is now routinely used to make vaccines and growth hormones for farm animals. Transgenic organisms with genes from another species have been developed to exploit the attributes of the new genes (for example, faster growth, larger muscles). Other transgenic organisms are pharmaceutical “factories” - a producer of large amounts of an otherwise rare substance for medical use. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.18

24. The human proteins produced by farm animals may or may not be structurally identical to natural human proteins. Therefore, they have to be tested very carefully to ensure that they will not cause allergic reactions or other adverse effects in patients receiving them. In addition, the health and welfare of transgenic farm animals are important issues, as they often suffer from lower fertility or increased susceptibility to disease. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

25. To develop a transgenic organism, scientists remove ova from a female and fertilize them in vitro. The desired gene from another organism are cloned and then inserted into the nuclei of the eggs. Some cells will integrate the foreign DNA into their genomes and are able to express its protein. The engineered eggs are then surgically implanted in a surrogate mother. If development is successful, the results is a transgenic animal, containing a genes from a “third” parent, even from another species. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

26. Agricultural scientists have engineered a number of crop plants with genes for desirable traits. These includes delayed ripening and resistance to spoilage and disease. Because a single transgenic plant cell can be grown in culture to generate an adult plant, plants are easier to engineer than most animals. The Ti plasmid, from the soil bacterium Agrobacterium tumefaciens, is often used to introduce new genes into plant cells. The Ti plasmid normally integrates a segment of its DNA into its host plant and induces tumors. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

27. Foreign genes can be inserted into the Ti plasmid (a version that does not cause disease) using recombinant DNA techniques. The recombinant plasmid can be put back into Agrobacterium, which then infects plant cells, or introduced directly into plant cells. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.19

28. The Ti plasmid can only be used as a vector to transfer genes to dicots (plants with two seed leaves). Monocots, including corn and wheat, cannot be infected by Agrobacterium (or the Ti plasmid). Other techniques, including electroporation and DNA guns, are used to introduce DNA into these plants. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

29. Genetic engineering is quickly replacing traditional plant-breeding programs. In the past few years, roughly half of the soybeans and corn in America have been grown from genetically modified seeds. These plants may receive genes for resistance to weed- killing herbicides or to infectious microbes and pest insects. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

30. Scientists are using gene transfer to improve the nutritional value of crop plants. For example, a transgenic rice plant has been developed that produces yellow grains containing beta-carotene. Humans use beta-carotene to make vitamin A. Currently, 70% of children under the age of 5 in Southeast Asia are deficient in vitamin A, leading to vision impairment and increased disease rates. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 20.20

31. An important potential use of DNA technology focuses on nitrogen fixation. Nitrogen fixation occurs when certain bacteria in the soil or in plant roots convert atmospheric nitrogen to nitrogen compounds that plants can use. Plants use these to build nitrogen-containing compounds, such as amino acids. In areas with nitrogen-deficient soils, expensive fertilizers must be added for crops to grow. Nitrogen fertilizers also contribute to water pollution. DNA technology offers ways to increase bacterial nitrogen fixation and eventually, perhaps, to engineer crop plants to fix nitrogen themselves. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

32. DNA technology has led to new alliances between the pharmaceutical industry and agriculture. Plants can be engineered to produce human proteins for medical use and viral proteins for use as vaccines. Several such “pharm” products are in clinical trials, including vaccines for hepatitis B and an antibody that blocks the bacteria that cause tooth decay. The advantage of “pharm” plants is that large amounts of these proteins might be made more economically by plants than by cultured cells. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

33. The power of DNA technology has led to worries about potential dangers. For example, recombinant DNA technology may create hazardous new pathogens. In response, scientists developed a set of guidelines that have become formal government regulations in the United States and some other countries. 3. DNA technology raises important safety and ethical questions Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

34. Strict laboratory procedures are designed to protect researchers from infection by engineered microbes and to prevent their accidental release. Some strains of microorganisms used in recombinant DNA experiments are genetically crippled to ensure that they cannot survive outside the laboratory. Finally, certain obviously dangerous experiments have been banned. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

35. Today, most public concern centers on genetically modified (GM) organisms used in agriculture. “GM organisms” have acquired one or more genes (perhaps from another species) by artificial means. Genetically modified animals are still not part of our food supply, but GM crop plants are. In Europe, safety concerns have led to pending new legislation regarding GM crops and bans on the import of all GM foodstuffs. In the United States and other countries where the GM revolution had proceeded more quietly, the labeling of GM foods is now being debated. This is required by exporters in a Biosafety Protocol. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

36. Advocates of a cautious approach fear that GM crops might somehow be hazardous to human health or cause ecological harm. In particular, transgenic plants may pass their new genes to close relatives in nearby wild areas through pollen transfer. Transference of genes for resistance to herbicides, diseases, or insect pests may lead to the development of wild “superweeds” that would be difficult to control. To date there is little good data either for or against any special health or environmental risks posed by genetically modified crops. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

37. Today, governments and regulatory agencies are grappling with how to facilitate the use of biotechnology in agriculture, industry, and medicine while ensuring that new products and procedures are safe. In the United States, all projects are evaluated for potential risks by various regulatory agencies, including the Environmental Protection Agency, the National Institutes of Health, and the Department of Agriculture. These agencies are under increasing pressures from some consumer groups. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

38. As with all new technologies, developments in DNA technology have ethical overtones. Who should have the right to examine someone else’s genes? How should that information be used? Should a person’s genome be a factor in suitability for a job or eligibility for life insurance? The power of DNA technology and genetic engineering demands that we proceed with humility and caution. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings